现代优化计算方法在蛋白质结构预测中的应用

现代优化计算方法在蛋白质结构预测中占有重要地位.简要地介绍了模拟退火算法,遗传算法,人工神经网络和图论算法在蛋白质结构预测中的应用.对国内外近年来应用这些算法,特别是在蛋白质构象搜索问题中,解决蛋白质结构预测的研究作了回顾,并分析、比较了这几种算法的效果和特点.     

实时任务动态调度算法

任务调度算法是提高多任务系统效率的一种有效途径,特别是在时间紧迫环境下,实时任务调度算法更具有重要的应用价值.在研究建立实时任务调度模型方法的基础上,对模型进行理论分析,提出了实时任务调度的算法,并通过实例加以验证.     

A note on the computational complexity of graph vertex partition

A stable set of a graph is a vertex set in which any two vertices are not adjacent. It was proven in [A. Brandstädt, V.B. Le, T. Szymczak, The complexity of some problems related to graph 3-colorability, Discrete Appl. Math. 89 (1998) 59-73] that the following problem is NP-complete: Given a bipartite graph G, check whether G has a stable set S such thatG-Sis a tree. In this paper we prove the following problem is polynomially solvable: Given a graph G with maximum degree 3 and containing no vertices of degree 2, check whether G has a stable set S such thatG-Sis a tree. Thus we partly answer a question posed by the authors in the above paper. Moreover, we give some structural characterizations for a graph G with maximum degree 3 that has a stable set S such that G-S is a tree.     

An approximate proximal-extragradient type method for monotone variational inequalities

Proximal point algorithms (PPA) are attractive methods for monotone variational inequalities. The approximate versions of PPA are more applicable in practice. A modified approximate proximal point algorithm (APPA) presented by Solodov and Svaiter [Math. Programming, Ser. B 88 (2000) 371–389] relaxes the inexactness criterion significantly. This paper presents an extended version of Solodov–Svaiter's APPA. Building the direction from current iterate to the new iterate obtained by Solodov–Svaiter's APPA, the proposed method improves the profit at each iteration by choosing the optimal step length along this direction. In addition, the inexactness restriction is relaxed further. Numerical example indicates the improvement of the proposed method.     

Compact directed acyclic word graphs for a sliding window

Suffix trees are a well-known and widely-studied data structure highly useful for string matching. The suffix tree of a string w can be constructed in O(n) time and space, where n denotes the length of w. Larsson achieved an efficient algorithm to maintain suffix trees for a sliding window. It contributes to prediction by partial matching (PPM) style statistical data compression scheme. Compact directed acyclic word graphs (CDAWGs) are a more space-economical data structure for indexing strings. In this paper we propose a linear-time algorithm to maintain CDAWGs for a sliding window.     

The Computational Complexity of the Chow Form

We present a bounded probability algorithm for the computation of the Chowforms of the equidimensional components of an algebraic variety. In particular, this gives an alternative procedure for the effective equidimensional decomposition of the variety, since each equidimensional component is characterized by its Chow form. The expected complexity of the algorithm is polynomial in the size and the geometric degree of the input equation system defining the variety. Hence it improves (or meets in some special cases) the complexity of all previous algorithms for computing Chow forms. In addition to this, we clarify the probability and uniformity aspects, which constitutes a further contribution of the paper. The algorithm is based on elimination theory techniques, in line with the geometric resolution algorithm due to M. Giusti, J. Heintz, L. M. Pardo, and their collaborators. In fact, ours can be considered as an extension of their algorithm for zero-dimensional systems to the case of positive-dimensional varieties. The key element for dealing with positive-dimensional varieties is a new Poisson-type product formula. This formula allows us to compute the Chow form of an equidimensional variety from a suitable zero-dimensional fiber. As an application, we obtain an algorithm to compute a subclass of sparse resultants, whose complexity is polynomial in the dimension and the volume of the input set of exponents. As another application, we derive an algorithm for the computation of the (unique) solution of a generic overdetermined polynomial equation system.     

Towards the Exact Minimization of BDDs—An Elitism-Based Distributed Evolutionary Algorithm

Binary Decision Diagrams (BDDs) are the state-of-the-art data structure for representation and manipulation of Boolean functions. In general, exact BDD minimization is NP-complete. For BDD-based technology, a small improvement in the number of nodes often simplifies the follow-up problem tremendously. This paper proposes an elitism-based evolutionary algorithm (EBEA) for BDD minimization. It can efficiently find the optimal orderings of variables for all LGSynth91 benchmark circuits with a known minimum size. Moreover, we develop a distributed model of EBEA, DEBEA, which obtains the best-ever variable orders for almost all benchmarks in the LGSynth91. Experimental results show that DEBEA is able to achieve super-linear performance compared to EBEA for some hard benchmarks.     

SASEGASA: A New Generic Parallel Evolutionary Algorithm for Achieving Highest Quality Results

This paper presents a new generic Evolutionary Algorithm (EA) for retarding the unwanted effects of premature convergence. This is accomplished by a combination of interacting generic methods. These generalizations of a Genetic Algorithm (GA) are inspired by population genetics and take advantage of the interactions between genetic drift and migration. In this regard a new selection scheme is introduced, which is designed to directedly control genetic drift within the population by advantageous self-adaptive selection pressure steering. Additionally this new selection model enables a quite intuitive heuristics to detect premature convergence. Based upon this newly postulated basic principle the new selection mechanism is combined with the already proposed Segregative Genetic Algorithm (SEGA), an advanced Genetic Algorithm (GA) that introduces parallelism mainly to improve global solution quality. As a whole, a new generic evolutionary algorithm (SASEGASA) is introduced. The performance of the algorithm is evaluated on a set of characteristic benchmark problems. Computational results show that the new method is capable of producing highest quality solutions without any problem-specific additions.     

Combining Swaps and Node Weights in an Adaptive Greedy Approach for the Maximum Clique Problem

In this work, the NP-hard maximum clique problem on graphs is considered. Starting from basic greedy heuristics, modifications and improvements are proposed and combined in a two-phase heuristic procedure. In the first phase an improved greedy procedure is applied starting from each node of the graph; on the basis of the results of this phase a reduced subset of nodes is selected and an adaptive greedy algorithm is repeatedly started to build cliques around such nodes. In each restart the selection of nodes is biased by the maximal clique generated in the previous execution. Computational results are reported on the DIMACS benchmarks suite. Remarkably, the two-phase procedure successfully solves the difficult Brockington-Culberson instances, and is generally competitive with state-of-the-art much more complex heuristics.     

Widrow-cellular neural network and optoelectronic implementation

A new type of optoelectronic cellular neural network has been developed by providing the capability of coefficients adjusment of cellular neural network (CNN) using Widrow based perceptron learning algorithm. The new supervised cellular neural network is called Widrow-CNN. Despite the unsupervised CNN, the proposed learning algorithm allows to use the Widrow-CNN for various image processing applications easily. Also, the capability of CNN for image processing and feature extraction has been improved using basic joint transform correlation architecture. This hardware application presents high speed processing capability compared to digital applications. The optoelectronic Widrow-CNN has been tested for classic CNN feature extraction problems. It yields the best results even in case of hard feature extraction problems such as diagonal line detection and vertical line determination.